Here is an interesting Tweet from actress Rachel Nichols, who basically confirmed she will not be returning for the G.I. Joe sequel and that Snake Eyes, Storm Shadow and Duke are the only returning characters.

Not too sure how you can have G.I. Joe team with out the other characters, but at the same time Snake Eyes and Storm Shadow are the two best characters. Some are speculating that the smaller budget for the movie is why there are only 3 returning cast members.